I have a cylinder with 5 sides and rotated 90° so I now have a flat side on the left, now in edit mode I select the 4 verts of that flat side and move it to the center with the origin point. Just like you would do with a cube. When I mirror the cylinder it doesn’t mirror on the X axis but mirrors on the Y axis?
you want to leave edit mode, hit ‘ctrl A’, and select apply rotation.